Variant report

Variant	rs6721860
Chromosome Location	chr2:38818221-38818222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38816751..38822030-chr2:38827238..38830922,5	MCF-7	breast:
2	chr2:38301826..38303354-chr2:38817276..38820176,2	MCF-7	breast:
3	chr2:38816136..38818407-chr2:38916717..38919701,2	K562	blood:
4	chr2:38816358..38820230-chr2:38976960..38979820,4	MCF-7	breast:
5	chr2:38816590..38821819-chr2:38825503..38830021,9	MCF-7	breast:
6	chr2:38818005..38820191-chr2:38893287..38895221,2	K562	blood:
7	chr2:38810772..38814090-chr2:38815738..38818660,3	MCF-7	breast:
8	chr2:38815999..38818648-chr2:38976723..38978521,3	K562	blood:
9	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000232973	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000138061	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10204680	0.94[JPT][hapmap]
rs12329205	0.87[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap]
rs13032371	0.82[ASN][1000 genomes]
rs13393767	0.85[ASN][1000 genomes]
rs13431551	0.93[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13432435	0.83[ASN][1000 genomes]
rs1368114	0.93[CHD][hapmap];0.96[GIH][hapmap];0.80[LWK][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs17022996	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17023003	0.87[CHD][hapmap];0.82[MKK][hapmap]
rs17493538	0.84[EUR][1000 genomes]
rs17493594	0.85[EUR][1000 genomes]
rs17575960	0.94[JPT][hapmap]
rs1864828	0.81[EUR][1000 genomes]
rs2099261	0.81[ASN][1000 genomes]
rs2116385	1.00[JPT][hapmap]
rs2163551	0.81[JPT][hapmap]
rs2217537	0.82[ASN][1000 genomes]
rs2253519	0.93[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2373421	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2373423	0.90[CHD][hapmap];0.83[JPT][hapmap]
rs34450185	0.83[ASN][1000 genomes]
rs36057155	0.90[ASN][1000 genomes]
rs56217714	0.80[EUR][1000 genomes]
rs56311849	0.81[EUR][1000 genomes]
rs6544169	0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6544170	0.84[EUR][1000 genomes]
rs6733950	0.87[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs6736320	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6742843	1.00[JPT][hapmap]
rs6745023	0.80[EUR][1000 genomes]
rs6745646	0.83[ASN][1000 genomes]
rs6757844	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7571463	1.00[CEU][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7573095	0.85[EUR][1000 genomes]
rs7609065	0.87[ASN][1000 genomes]
rs891706	0.88[ASN][1000 genomes]
rs919698	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
3	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
4	chr2:38782400-38819000	Strong transcription	Fetal Thymus	thymus
5	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
8	chr2:38786400-38818800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:38786600-38819000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:38798000-38827600	Weak transcription	Spleen	Spleen
11	chr2:38798200-38820600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:38798200-38821800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:38798800-38822000	Weak transcription	NHEK	skin
15	chr2:38799800-38827800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:38800000-38818600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:38802800-38819000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:38805200-38826400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:38807200-38819000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:38808200-38824400	Weak transcription	Hela-S3	cervix
21	chr2:38808400-38820400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:38808800-38819000	Strong transcription	Dnd41	blood
23	chr2:38808800-38821800	Weak transcription	HMEC	breast
24	chr2:38808800-38825200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:38808800-38825400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:38808800-38827000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:38808800-38827400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:38808800-38827400	Weak transcription	Pancreas	Pancrea
29	chr2:38809000-38819600	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:38809000-38824200	Weak transcription	Liver	Liver
31	chr2:38809000-38825600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr2:38809400-38825800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:38809600-38827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:38810000-38827600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:38811600-38819600	Weak transcription	NH-A	brain
36	chr2:38811800-38819600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:38812200-38818600	Strong transcription	K562	blood
38	chr2:38812600-38823800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:38813000-38819600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:38813000-38821800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:38813000-38821800	Weak transcription	Adipose Nuclei	Adipose
42	chr2:38813000-38823800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:38813200-38819800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:38813200-38826000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:38813400-38827000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:38813800-38825400	Weak transcription	Primary T cells from cord blood	blood
47	chr2:38814400-38825200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:38814400-38825600	Weak transcription	HUVEC	blood vessel
49	chr2:38814600-38824200	Weak transcription	Fetal Brain Female	brain
50	chr2:38815200-38824000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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